Bactopia: a Flexible Pipeline for Complete Analysis of Bacterial Genomes.

ABSTRACT: Sequencing of bacterial genomes using Illumina technology has become such a standard procedure that often data are generated faster than can be conveniently analyzed. We created a new series of pipelines called Bactopia, built using Nextflow workflow software, to provide efficient comparative genomic analyses for bacterial species or genera. Bactopia consists of a data set setup step (Bactopia Data Sets [BaDs]), which creates a series of customizable data sets for the species of interest, the Bactopia Analysis Pipeline (BaAP), which performs quality control, genome assembly, and several other functions based on the available data sets and outputs the processed data to a structured directory format, and a series of Bactopia Tools (BaTs) that perform specific postprocessing on some or all of

SUBMITTER: Petit RA 

PROVIDER: S-EPMC7406220 | biostudies-literature | 2020 Aug

REPOSITORIES: biostudies-literature